Class picard.analysis.directed.CollectTargetedMetricsTest
Tests
| Test |
Duration |
Result |
| runCollectTargetedMetricsTest[0](testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics2039798244537543153.bam, /tmp/test7963807332351051637.TargetedMetrics_Coverage, /tmp/perTarget4835373909528693993.perTargetCoverage, testdata/picard/quality/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000) |
1.046s |
passed |
| runCollectTargetedMetricsTest[1](testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics2039798244537543153.bam, /tmp/test7963807332351051637.TargetedMetrics_Coverage, /tmp/perTarget4835373909528693993.perTargetCoverage, testdata/picard/quality/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000) |
0.745s |
passed |
Standard error
[Tue Aug 16 04:11:26 CDT 2016] picard.analysis.directed.CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics2039798244537543153.bam OUTPUT=/tmp/test7963807332351051637.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget4835373909528693993.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:26 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:27 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:27 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:27 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:27 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2016-08-16 04:11:27 TargetMetricsCollector Calculating GC metrics
[Tue Aug 16 04:11:27 CDT 2016] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:27 CDT 2016] picard.analysis.directed.CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.empty.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.empty.interval_list] INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CollectGcBiasMetrics/CollectTargetedMetrics2039798244537543153.bam OUTPUT=/tmp/test7963807332351051637.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget4835373909528693993.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=testdata/picard/quality/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:27 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:28 TheoreticalSensitivity Creating Roulette Wheel
INFO 2016-08-16 04:11:28 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2016-08-16 04:11:28 TheoreticalSensitivity 0 sampling iterations completed
INFO 2016-08-16 04:11:28 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2016-08-16 04:11:28 TargetMetricsCollector Calculating GC metrics
WARNING 2016-08-16 04:11:28 TargetMetricsCollector interval of length zero found: chrM:2-1 + interval-1 skipped.
[Tue Aug 16 04:11:28 CDT 2016] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1830289408